Dancing with the Stars finds the best dancer out of the group, even if they're not pros. Survivor ostensibly finds the best survivor out of the group, even if they're not true outdoorsmen.
Reality TV is the same - except the fiction is the competition isn't rigged and its primary goal is to find the best candidate. The show doesn't wildly contradict it, it's just not true.
Looking at the strips after the fact, Abby and Katie pretty obviously are writing the best strips. And sure, Abby's is the better of the two, but her concept is harder to distill down to its essence and present - Katie was the only one of the three finalists who was able to competently and interestingly introduce her new strip with just a few sample pages.
If you think they picked wrong, who should have won instead?
(Note that several of the other cartoonists have been hired by Penny Arcade for other tasks such as doing The Trenches and designing pins. So even if you ignore the publicity aspect there were still multiple winners.)
Of the last two, Abby should have won IMO.